CSeqTableInfo Class Reference

Search Toolkit Book for CSeqTableInfo

#include <objmgr/impl/seq_table_info.hpp>

Inheritance diagram for CSeqTableInfo:

Collaboration diagram for CSeqTableInfo:

Public Member Functions
	CSeqTableInfo (const CSeq_table &feat_table, bool is_feat)
	CSeqTableInfo (const CSeq_table &feat_table)
	~CSeqTableInfo ()
bool	IsFeatTable (void) const
size_t	GetNumRows (void) const
void	UpdateSeq_feat (size_t row, CRef< CSeq_feat > &seq_feat, CRef< CSeq_point > &seq_pnt, CRef< CSeq_interval > &seq_int) const
CConstRef< CSeq_loc >	GetTableLocation (void) const
TSeqPos	GetSortedMaxLength (void) const
bool	IsSorted (void) const
SAnnotTypeSelector	GetType (void) const
const CSeqTableLocColumns &	GetLocation (void) const
const CSeqTableLocColumns &	GetProduct (void) const
bool	RowIsDisabled (size_t row) const
bool	IsPartial (size_t row) const
CConstRef< CSeq_id >	GetLocationId (size_t row) const
TSeqPos	GetLocationFrom (size_t row) const
CRange< TSeqPos >	GetLocationRange (size_t row) const
ENa_strand	GetLocationStrand (size_t row) const
bool	HasLabel (size_t row) const
string	GetLabel (size_t row) const
bool	MatchBitFilter (const SAnnotSelector &sel, size_t row) const
const CSeqTableColumnInfo *	FindColumn (int field_id) const
const CSeqTableColumnInfo *	FindColumn (const string &field_name) const
const CSeqTableColumnInfo &	GetColumn (int field_id) const
const CSeqTableColumnInfo &	GetColumn (const string &field_name) const
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Static Public Member Functions
static bool	IsGoodFeatTable (const CSeq_table &table)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Private Types
typedef CSeqTableSetFeatField	TSetter
typedef pair< CSeqTableColumnInfo, CConstRef< TSetter > >	TColumnInfo
typedef vector< TColumnInfo >	TExtraColumns
typedef map< int, CSeqTableColumnInfo >	TColumnsById
typedef map< string, CSeqTableColumnInfo >	TColumnsByName

Private Member Functions
void	x_Initialize (const CSeq_table &table)
bool	x_IsSorted (void) const
	CSeqTableInfo (const CSeqTableInfo &)
void	operator= (const CSeqTableInfo &)

Private Attributes
CConstRef< CSeq_table >	m_Seq_table
bool	m_IsFeatTable
bool	m_IsSorted
CSeqTableColumnInfo	m_Disabled
CSeqTableLocColumns	m_Location
CSeqTableLocColumns	m_Product
CSeqTableColumnInfo	m_Partial
TExtraColumns	m_ExtraColumns
CConstRef< CSeq_loc >	m_TableLocation
TSeqPos	m_SortedMaxLength
TColumnsById	m_ColumnsById
TColumnsByName	m_ColumnsByName

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 206 of file seq_table_info.hpp.

Member Typedef Documentation

TColumnInfo

typedef pair<CSeqTableColumnInfo, CConstRef<TSetter> > CSeqTableInfo::TColumnInfo

private

Definition at line 277 of file seq_table_info.hpp.

TColumnsById

typedef map<int, CSeqTableColumnInfo> CSeqTableInfo::TColumnsById

private

Definition at line 295 of file seq_table_info.hpp.

TColumnsByName

typedef map<string, CSeqTableColumnInfo> CSeqTableInfo::TColumnsByName

private

Definition at line 296 of file seq_table_info.hpp.

TExtraColumns

typedef vector<TColumnInfo> CSeqTableInfo::TExtraColumns

private

Definition at line 278 of file seq_table_info.hpp.

TSetter

typedef CSeqTableSetFeatField CSeqTableInfo::TSetter

private

Definition at line 276 of file seq_table_info.hpp.

Constructor & Destructor Documentation

CSeqTableInfo() [1/3]

CSeqTableInfo::CSeqTableInfo ( const CSeq_table &  feat_table, bool  is_feat  )

explicit

Definition at line 766 of file seq_table_info.cpp.

References x_Initialize().

CSeqTableInfo() [2/3]

CSeqTableInfo::CSeqTableInfo ( const CSeq_table &  feat_table )

explicit

Definition at line 775 of file seq_table_info.cpp.

References x_Initialize().

~CSeqTableInfo()

CSeqTableInfo::~CSeqTableInfo

(

)

Definition at line 949 of file seq_table_info.cpp.

CSeqTableInfo() [3/3]

CSeqTableInfo::CSeqTableInfo ( const CSeqTableInfo &  )

private

Member Function Documentation

FindColumn() [1/2]

const CSeqTableColumnInfo * CSeqTableInfo::FindColumn

(

const string &

field_name

)

const

Definition at line 1126 of file seq_table_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and m_ColumnsByName.

FindColumn() [2/2]

const CSeqTableColumnInfo * CSeqTableInfo::FindColumn

(

int

field_id

)

const

Definition at line 1115 of file seq_table_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and m_ColumnsById.

Referenced by GetColumn(), and CTableFieldHandle_Base::x_FindColumn().

GetColumn() [1/2]

const CSeqTableColumnInfo & CSeqTableInfo::GetColumn

(

const string &

field_name

)

const

Definition at line 1150 of file seq_table_info.cpp.

References column, FindColumn(), and NCBI_THROW_FMT.

GetColumn() [2/2]

const CSeqTableColumnInfo & CSeqTableInfo::GetColumn

(

int

field_id

)

const

Definition at line 1137 of file seq_table_info.cpp.

References column, FindColumn(), and NCBI_THROW_FMT.

GetLabel()

string CSeqTableInfo::GetLabel

(

size_t

row

)

const

Definition at line 1067 of file seq_table_info.cpp.

References CSeqTable_column_info_Base::GetField_name(), CSeqTable_column_Base::GetHeader(), CSeqTable_column_info_Base::IsSetField_name(), m_ExtraColumns, and str().

Referenced by CSeq_annot_Info::TableFeat_GetLabel().

GetLocation()

const CSeqTableLocColumns& CSeqTableInfo::GetLocation ( void  ) const

inline

Definition at line 235 of file seq_table_info.hpp.

References m_Location.

Referenced by GetLocationFrom(), GetLocationId(), GetLocationRange(), GetLocationStrand(), CSeq_annot_Info::UpdateTableFeatLocation(), and CSeq_annot_Info::x_InitFeatTableKeys().

GetLocationFrom()

TSeqPos CSeqTableInfo::GetLocationFrom ( size_t  row ) const

inline

Definition at line 251 of file seq_table_info.hpp.

References CSeqTableLocColumns::GetFrom(), GetLocation(), and row.

Referenced by CSeq_annot_Info::StartSortedIterator().

GetLocationId()

CConstRef<CSeq_id> CSeqTableInfo::GetLocationId ( size_t  row ) const

inline

Definition at line 248 of file seq_table_info.hpp.

References CSeqTableLocColumns::GetId(), GetLocation(), and row.

Referenced by CAnnotObject_Ref::CAnnotObject_Ref().

GetLocationRange()

CRange<TSeqPos> CSeqTableInfo::GetLocationRange ( size_t  row ) const

inline

Definition at line 254 of file seq_table_info.hpp.

References GetLocation(), CSeqTableLocColumns::GetRange(), and row.

Referenced by CSeq_annot_SortedIter::x_Valid().

GetLocationStrand()

ENa_strand CSeqTableInfo::GetLocationStrand ( size_t  row ) const

inline

Definition at line 257 of file seq_table_info.hpp.

References GetLocation(), CSeqTableLocColumns::GetStrand(), and row.

Referenced by CAnnotObject_Ref::CAnnotObject_Ref().

GetNumRows()

size_t CSeqTableInfo::GetNumRows ( void  ) const

inline

Definition at line 217 of file seq_table_info.hpp.

References CSeq_table_Base::GetNum_rows(), and m_Seq_table.

Referenced by CSeq_annot_Info::StartSortedIterator().

GetProduct()

const CSeqTableLocColumns& CSeqTableInfo::GetProduct ( void  ) const

inline

Definition at line 238 of file seq_table_info.hpp.

References m_Product.

Referenced by CSeq_annot_Info::UpdateTableFeatProduct(), and CSeq_annot_Info::x_InitFeatTableKeys().

GetSortedMaxLength()

TSeqPos CSeqTableInfo::GetSortedMaxLength

(

void

)

const

Definition at line 972 of file seq_table_info.cpp.

References m_SortedMaxLength.

Referenced by CSeq_annot_Info::StartSortedIterator().

GetTableLocation()

CConstRef< CSeq_loc > CSeqTableInfo::GetTableLocation

(

void

)

const

Definition at line 966 of file seq_table_info.cpp.

References m_TableLocation.

Referenced by CSeq_table_CI::GetOriginalLocation(), and CSeq_annot_Info::x_InitFeatTableKeys().

GetType()

SAnnotTypeSelector CSeqTableInfo::GetType

(

void

)

const

Definition at line 954 of file seq_table_info.cpp.

References _ASSERT, IsFeatTable(), m_Seq_table, table, and type.

Referenced by CSeq_feat_Handle::GetFeatSubtype(), CSeq_feat_Handle::GetFeatType(), CAnnotObjectType_Less::operator()(), and CSeq_annot_Info::x_InitFeatTable().

HasLabel()

bool CSeqTableInfo::HasLabel

(

size_t

row

)

const

Definition at line 1051 of file seq_table_info.cpp.

References CSeqTable_column_info_Base::GetField_name(), CSeqTable_column_Base::GetHeader(), CSeqTable_column_info_Base::IsSetField_name(), and m_ExtraColumns.

Referenced by CSeq_annot_Info::TableFeat_HasLabel().

IsFeatTable()

bool CSeqTableInfo::IsFeatTable ( void  ) const

inline

Definition at line 213 of file seq_table_info.hpp.

References m_IsFeatTable.

Referenced by GetType(), CSeq_annot_Info::x_InitFeatTableKeys(), and x_Initialize().

IsGoodFeatTable()

bool CSeqTableInfo::IsGoodFeatTable ( const CSeq_table &  table )

static

Definition at line 750 of file seq_table_info.cpp.

References CSeqFeatData_Base::e_MaxChoice, CSeqFeatData_Base::e_not_set, CSeqFeatData::eSubtype_bad, CSeqFeatData::eSubtype_max, and table.

Referenced by CBlobSplitterImpl::CopyAnnot(), and CSeq_annot_Info::x_InitFeatTable().

IsPartial()

bool CSeqTableInfo::IsPartial ( size_t  row ) const

inline

Definition at line 244 of file seq_table_info.hpp.

References CSeqTableColumnInfo::GetBool(), m_Partial, and row.

Referenced by CSeq_annot_Info::IsTableFeatPartial(), and CSeq_annot_Info::x_InitFeatTableKeys().

IsSorted()

bool CSeqTableInfo::IsSorted ( void  ) const

inline

Definition at line 229 of file seq_table_info.hpp.

References m_IsSorted.

Referenced by CSeq_annot_Info::IsSortedTable().

MatchBitFilter()

bool CSeqTableInfo::MatchBitFilter	(	const SAnnotSelector &	sel,
		size_t	row
	)		const

Definition at line 1091 of file seq_table_info.cpp.

References CSeqTable_column_info_Base::GetField_name(), SAnnotSelector::GetFilterBits(), SAnnotSelector::GetFilterMask(), CSeqTable_column_Base::GetHeader(), CSeqTable_column_info_Base::IsSetField_name(), and m_ExtraColumns.

Referenced by CSeq_annot_Info::MatchBitFilter().

operator=()

void CSeqTableInfo::operator= ( const CSeqTableInfo &  )

private

RowIsDisabled()

bool CSeqTableInfo::RowIsDisabled ( size_t  row ) const

inline

Definition at line 241 of file seq_table_info.hpp.

References CSeqTableColumnInfo::GetBool(), m_Disabled, and row.

Referenced by CSeq_annot_Info::x_InitFeatTableKeys(), and CSeq_annot_SortedIter::x_Valid().

UpdateSeq_feat()

void CSeqTableInfo::UpdateSeq_feat	(	size_t	row,
		CRef< CSeq_feat > &	seq_feat,
		CRef< CSeq_point > &	seq_pnt,
		CRef< CSeq_interval > &	seq_int
	)		const

Definition at line 1009 of file seq_table_info.cpp.

References CSeqTableColumnInfo::GetValue(), CSeqTableLocColumns::IsSet(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetProduct(), ITERATE, m_ExtraColumns, m_Location, m_Partial, m_Product, CSeq_feat_Base::Reset(), row, CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), CSeq_feat_Base::SetProduct(), CSeqTableLocColumns::UpdateSeq_loc(), and val.

Referenced by CCreateFeat::GetOriginalFeat(), CCreatedFeat_Ref::GetOriginalFeature(), and CSeq_annot_Info::UpdateTableFeat().

x_Initialize()

void CSeqTableInfo::x_Initialize ( const CSeq_table &  table )

private

Definition at line 784 of file seq_table_info.cpp.

References CSeqTableLocColumns::AddColumn(), CSeqTable_column_info_Base::eField_id_comment, CSeqTable_column_info_Base::eField_id_data_imp_key, CSeqTable_column_info_Base::eField_id_data_region, CSeqTable_column_info_Base::eField_id_dbxref, CSeqTable_column_info_Base::eField_id_ext, CSeqTable_column_info_Base::eField_id_ext_type, CSeqTable_column_info_Base::eField_id_partial, CSeqTable_column_info_Base::eField_id_qual, CTempString::empty(), ERR_POST, ERR_POST_X, CSeq_table_Base::GetColumns(), CSeqTable_column_Base::GetHeader(), info, map_checker< Container >::insert(), IsFeatTable(), ITERATE, m_ColumnsById, m_ColumnsByName, m_Disabled, m_ExtraColumns, m_IsSorted, m_Location, m_Partial, m_Product, m_Seq_table, m_SortedMaxLength, m_TableLocation, NCBI_CATCH, NCBI_THROW_FMT, CSeqTableLocColumns::ParseDefaults(), rapidjson::value, and x_IsSorted().

Referenced by CSeqTableInfo().

x_IsSorted()

bool CSeqTableInfo::x_IsSorted ( void  ) const

private

Definition at line 978 of file seq_table_info.cpp.

References CSeq_loc_Base::GetInt(), CSeq_interval::GetLength(), CSeq_loc_Base::IsInt(), CSeqTableLocColumns::IsRealLoc(), CSeqTableLocColumns::IsSet(), CSeqTableColumnInfo::IsSingular(), CSeqTableLocColumns::m_Id, CSeqTableLocColumns::m_Is_simple, CSeqTableLocColumns::m_Is_simple_interval, CSeqTableLocColumns::m_Is_simple_point, m_Location, m_Product, m_SortedMaxLength, and m_TableLocation.

Referenced by x_Initialize().

Member Data Documentation

m_ColumnsById

TColumnsById CSeqTableInfo::m_ColumnsById

private

Definition at line 297 of file seq_table_info.hpp.

Referenced by FindColumn(), and x_Initialize().

m_ColumnsByName

TColumnsByName CSeqTableInfo::m_ColumnsByName

private

Definition at line 298 of file seq_table_info.hpp.

Referenced by FindColumn(), and x_Initialize().

m_Disabled

CSeqTableColumnInfo CSeqTableInfo::m_Disabled

private

Definition at line 286 of file seq_table_info.hpp.

Referenced by RowIsDisabled(), and x_Initialize().

m_ExtraColumns

TExtraColumns CSeqTableInfo::m_ExtraColumns

private

Definition at line 290 of file seq_table_info.hpp.

Referenced by GetLabel(), HasLabel(), MatchBitFilter(), UpdateSeq_feat(), and x_Initialize().

m_IsFeatTable

bool CSeqTableInfo::m_IsFeatTable

private

Definition at line 284 of file seq_table_info.hpp.

Referenced by IsFeatTable().

m_IsSorted

bool CSeqTableInfo::m_IsSorted

private

Definition at line 285 of file seq_table_info.hpp.

Referenced by IsSorted(), and x_Initialize().

m_Location

CSeqTableLocColumns CSeqTableInfo::m_Location

private

Definition at line 287 of file seq_table_info.hpp.

Referenced by GetLocation(), UpdateSeq_feat(), x_Initialize(), and x_IsSorted().

m_Partial

CSeqTableColumnInfo CSeqTableInfo::m_Partial

private

Definition at line 289 of file seq_table_info.hpp.

Referenced by IsPartial(), UpdateSeq_feat(), and x_Initialize().

m_Product

CSeqTableLocColumns CSeqTableInfo::m_Product

private

Definition at line 288 of file seq_table_info.hpp.

Referenced by GetProduct(), UpdateSeq_feat(), x_Initialize(), and x_IsSorted().

m_Seq_table

CConstRef<CSeq_table> CSeqTableInfo::m_Seq_table

private

Definition at line 283 of file seq_table_info.hpp.

Referenced by GetNumRows(), GetType(), and x_Initialize().

m_SortedMaxLength

TSeqPos CSeqTableInfo::m_SortedMaxLength

private

Definition at line 293 of file seq_table_info.hpp.

Referenced by GetSortedMaxLength(), x_Initialize(), and x_IsSorted().

m_TableLocation

CConstRef<CSeq_loc> CSeqTableInfo::m_TableLocation

private

Definition at line 292 of file seq_table_info.hpp.

Referenced by GetTableLocation(), x_Initialize(), and x_IsSorted().

---

The documentation for this class was generated from the following files:

• include/objmgr/impl/seq_table_info.hpp
• src/objmgr/seq_table_info.cpp